GlassFish 3.1 : auto-upgrade or not to auto-upgrade?
By alexismp on Mar 09, 2011
This will do an In-Place Upgrade with the new bits (some 75MB pulled off of the stable.glassfish.org repository for the open source edition for instance).
You can of course also chose a Side-By-Side Upgrade. Both approaches are documented in the Upgrade Guide.
If you've installed GlassFish 3.0.1 as part of a NetBeans bundle such as 6.9(.1) you probably should not blindly update and rather use the recommended NetBeans 7.0 beta 2 for GlassFish 3.1. To stop the pop-up notification you can also use the Update Tool to disable it altogether, leaving you to manually check for updates.
If you intend to stay with 3.0.1, keep an eye on the GlassFishForBusiness blog for associated patch updates.